That's kind of strange. I've noticed the Dock can be strange at time. On my old PB, the trash would appear empty after a reboot until I opened it to reveal it's contents.
Nothing I did could fix this. It doesn't do it on my new PB though, nor did it ever do it on my Cube.
One thing I noticed when trying to isolate this problem is that Aqua is fighting really hard to coexist with it's UNIX core. Kind of like Windows 98 on top of DOS.
I won't go into detail but Apple has done a lot of things with OS X that aren't UNIX POSIX standard to retain it's OS 9 likeness, like the way programs are installed. I can see where this might cause things like the Dock and folders to goof up at times.
Hopefully there is over all better GUI and OS intergration in OS X "Jaguar."
All I can think is the Dock crashed, which it can, and restarted itself automatically, which it does, without those icons.